The goal of the Molecular Aspects of Drug Design Section is to discover new approaches to the design of drugs against cancer and viral diseases, especially AIDS. The general strategy is to integrate information obtained from biological and molecular studies of disease development with structural data on potential drug targets to design new drugs with greater effectiveness and lower systemic toxicity. Our specific approach is to combine mechanistic, computational, and synthetic chemistry with biochemical/biophysical and biological studies of the candidate drugs. DNA is an attractive target for chemotherapy because of its central role in the life of a cell. The repair of DNA damage is critical to the survival of a cell, whether normal or cancerous. The transcription of DNA into RNA, and the replication of DNA are also essential functions. Thus, in principle, selective targeting of these functions in tumor cells by small molecules may result in novel and highly selective drugs. We have found that the bifunctional agents bisimidazoacridones and the closely related bistriazoloacridones (collectively referred to as BIAs), which were discovered in our laboratory, appear to inhibit the growth human colon cancer cells in tissue culture and in nude mice by blocking the ability of the tumor cells to enter into mitosis. The binding of BIAs to the cellular DNA is recognized as damage that results in a cascade of biochemical events that block the progression of the cell through the cell cycle. If the arrested cells are then treated with inhibitors of cyclin-dependent kinases, which have the effect of forcing the cells to proceed into mitosis, the tumor cells die. The binding of BIAs to DNA involves both intercalation and minor groove binding. We hypothesized that one of the consequences of this mode of binding is the ability of the complex to capture a critical protein involved in repair of DNA damage or in transcription. Consideration of this hypothesis led us to propose that some Bias may be inhibitors of HIV replication. Indeed, several members of the series, especially one molecule now called temacrazine were found to have very potent anti-HIV activity. It was found that the molecular target for temacrazine is a component of transcriptional initiation. Thus, temacrazine and its congeners represent a novel class of potential drugs against HIV. The mode of binding of Bias to DNA led us to design a new class of compounds, represented by the unsymmetrical molecule WMC79, which retain many of the selectivity properties of the original Bias but are now potently cytotoxic to tumor cells. Again, the sensitive cells respond to a DNA damage signal. If the tumor cells contain un-mutated p53 tumor suppressor gene, the tumors die by apoptosis induced by p53-mediated activation of caspase 3. However, some tumors in which p53 is mutated or is not expressed are also highly sensitive to WMC79. These include some leukemia's and pancreatic cancers. These tumors are also killed by apoptosis, but the signaling pathways that lead to cell death are independent of p53. The targeting of drugs to specific receptors on tumor cells is a conceptually attractive method to enhance specificity and to decrease systemic toxicity. We have chosen the gastrin receptor (GR) as a prototype to test this hypothesis. Our work has shown that GR, a member of the G-protein-coupled receptor (GPCR) superfamily, undergoes endocytosis via clathrin-coated pits, is transported to the lysosomes, and recycles to the cell surface. Gastrin, the ligand for GR, is a peptide hormone that can be readily modified, because only the C-terminal tetrapeptide is required for recognition by the receptor. We have attached several cytotoxic moieties to various gastrin-derived peptides. Some of these conjugates have been shown to be very cytotoxic in GR+ cells but relatively benign in GR- cells. The immediate goal of this project is to further define the characteristics of an effective receptor-targeted drug by using the GR model. The results of these studies should be applicable to many other receptors. The techniques used for measuring trafficking of GR have been applied successfully to study the trafficking of other G-protein-coupled receptors, such as the cholecystokinin receptor type A and the chemokine receptors required for HIV entry into target cells. GPCRs are membrane proteins characterized by seven helical transmembrane (TM) domains. Other important polytopic membrane proteins include ABC transporters, some of which are responsible for the resistance of cancer and other diseases to drugs. We discovered that properly oriented synthetic peptides that correspond in sequence to a TM domain of a polytopic membrane protein are frequently able to inhibit the function of that protein with extraordinary specificity. For example, some peptides derived from the TM domains of the chemokine receptor CXCR4 are able to inhibit signaling and to block CXCR4-dependent HIV virus entry into cells at nanomolar concentrations. Similarly, specific peptides are also able to block the function of ABC transporters and block their ability to pump molecules out of tumor cells. This is a novel paradigm for drug discovery because it allows us to design specific agents that block the function of specific proteins without the knowledge of the tertiary structure of the proteins. Reverse transcription of the HIV RNA genome by reverse transcriptase (RT) is a step in viral replication that is absolutely required. Thus, RT has been an attractive target for drug design. Unfortunately, effective inhibitors of wild-type HIV RT are usually rapidly rendered ineffective by mutations in the enzyme. We have been searching for a new generation of inhibitors that will be active against mutant forms of RT. Our approach utilizes a combination of structural, molecular, modeling, and synthetic methodologies to gain a fundamental understanding of how this very complex enzyme carries out its function, and how the function may be disrupted. Some new, potent inhibitors of RT based on the 1,2-di-substituted benzimidazole nucleus have been designed and synthesized. Some of them inhibit many of the variant forms of RT and are potent inhibitors of the virus in infected cells. Interstitial cystitis (IC) is a devastating bladder disease that afflicts about 1 million Americans. While its etiology is not fully understood, we have isolated, identified and sythesized an antiproliferative factor (APF) from the bladder epithelium of IC patients. This research, which is in close collaboration with Dr. Susan Keay of the University of Maryland School of Medicine, will provide for the first time a specific diagnostic tool for IC and also suggests a method for its treatment. APF also potently inhibits the growth of bladder cancer cells and perhaps other tumors of epithelial origin.